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- PDB-7oxg: ttSlyD FKBP domain with M8A pseudo-wild-type S2 peptide -

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Basic information

Entry
Database: PDB / ID: 7oxg
TitlettSlyD FKBP domain with M8A pseudo-wild-type S2 peptide
Components
  • 30S ribosomal protein S2
  • Peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / FKBP
Function / homology
Function and homology information


RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / ribosomal small subunit assembly / protein refolding / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2 signature 1. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2
Similarity search - Domain/homology
IMIDAZOLE / Small ribosomal subunit protein uS2 / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPazicky, S. / Lei, J. / Loew, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
Joachim Herz Stiftung800026 Germany
German Federal Ministry for Education and Research05K18YEA Germany
CitationJournal: Cell.Mol.Life Sci. / Year: 2022
Title: Impact of distant peptide substrate residues on enzymatic activity of SlyD.
Authors: Pazicky, S. / Werle, A.A. / Lei, J. / Low, C. / Weininger, U.
History
DepositionJun 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase
B: Peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase
C: 30S ribosomal protein S2
D: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9297
Polymers27,7894
Non-polymers1403
Water1,17165
1
A: Peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase
C: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9994
Polymers13,8952
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-19 kcal/mol
Surface area6890 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase
D: 30S ribosomal protein S2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9303
Polymers13,8952
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-17 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.681, 82.525, 42.268
Angle α, β, γ (deg.)90.00, 110.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase,Peptidyl-prolyl cis-trans isomerase


Mass: 12179.549 Da / Num. of mol.: 2 / Mutation: Deletion of IF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0346 / Plasmid: pET11a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide 30S ribosomal protein S2 / Small ribosomal subunit protein uS2


Mass: 1714.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (strain K12) (bacteria) / References: UniProt: P0A7V0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 292.15 K / Method: counter-diffusion / pH: 5.5 / Details: Bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→39.59 Å / Num. obs: 15015 / % possible obs: 99.38 % / Redundancy: 4.8 % / Biso Wilson estimate: 31.43 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1084 / Rpim(I) all: 0.05427 / Rrim(I) all: 0.1216 / Net I/σ(I): 9.89
Reflection shellResolution: 2→2.072 Å / Redundancy: 5 % / Rmerge(I) obs: 0.9471 / Num. unique obs: 1467 / CC1/2: 0.696 / Rpim(I) all: 0.4619 / % possible all: 99.39

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cgm

3cgm


Resolution: 2→39.59 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 765 5.08 %
Rwork0.2023 --
obs0.2046 15063 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 7 65 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051828
X-RAY DIFFRACTIONf_angle_d0.9282478
X-RAY DIFFRACTIONf_dihedral_angle_d17.383241
X-RAY DIFFRACTIONf_chiral_restr0.054266
X-RAY DIFFRACTIONf_plane_restr0.006327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.33811470.29272790X-RAY DIFFRACTION98
2.15-2.370.30051580.26482864X-RAY DIFFRACTION99
2.37-2.710.29191770.23822839X-RAY DIFFRACTION99
2.71-3.410.24541450.19642880X-RAY DIFFRACTION99
3.41-41.260.1991380.16552925X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.22011.3544-0.42352.7192-2.32922.3427-0.05190.0055-0.0146-0.2196-0.1269-0.7685-0.12930.17040.21290.18030.00460.01110.22980.01330.250810.939320.92421.0764
22.16061.39191.02847.9406-1.50541.2658-0.0610.05870.08770.04730.09830.19040.1051-0.04430.01710.1870.00680.06590.2321-0.00880.14974.702717.57231.3707
33.941.0935-3.79817.4748-0.90253.8230.20080.02670.9980.5610.0755-0.6685-0.4740.3578-0.25820.28770.0125-0.09730.31060.05450.345914.206921.29886.2057
41.28220.7813-1.45482.857-1.41068.90660.5482-0.1898-0.08590.1885-0.55560.00820.2541-0.3633-0.02210.2828-0.02140.05240.2243-0.04720.26885.651711.85468.599
53.6878-1.9399-1.35426.58251.19970.8817-0.06720.37271.27490.1750.36751.41360.3841-0.707-0.14330.3875-0.07290.04150.46120.09490.5126-6.30696.56945.8316
66.26562.6151-3.65733.819-5.00376.8223-0.35110.1374-0.4245-0.4638-0.1068-0.78320.42860.20530.46070.1761-0.01870.00990.2466-0.02590.188711.770218.29710.6334
72.6096-2.0844-2.03945.55712.15431.76020.18670.16330.7314-0.4397-0.25540.137-0.6527-0.09110.10490.34350.0174-0.02810.19590.00160.37834.289435.0167-3.7705
89.32532.7652-0.76815.9904-1.72074.2692-0.47-0.22040.1624-0.61360.17260.19890.33520.17380.2610.42410.0538-0.040.2277-0.00780.132112.7349.14221.6933
97.35243.48-1.46966.8203-3.80073.58420.1778-0.31510.32780.3462-0.3953-0.3609-0.04441.00110.0270.3901-0.0116-0.08670.4742-0.02120.30319.524716.207925.3542
106.40013.1278-3.79879.05270.60759.711-0.20420.24250.4783-0.21710.36210.6857-0.514-0.7794-0.36490.35670.0564-0.10580.34130.03720.38136.299914.790422.46
112.34481.0634-1.24452.4774-3.97656.732-0.45460.25440.1034-0.35730.5028-0.30061.43520.30250.02320.5899-0.0384-0.08680.3997-0.04870.360414.047910.606114.1925
123.0498-0.2673-2.1165.3-2.24978.181-0.7649-0.44581.2326-0.0442-1.19830.5645-1.9648-1.57121.17830.95180.0245-0.34120.4728-0.07810.74613.718130.210522.0288
135.97252.2367-2.17868.7748-3.36377.6762-0.38240.2764-0.315-0.1110.0838-0.38270.68410.28080.20180.44240.0433-0.02320.32330.00160.165515.1148.55820.5394
141.5870.77811.18493.23913.87225.2952-0.7131-2.0055-1.37410.53730.19321.08121.1320.4750.77890.42760.05540.16860.50650.11570.64231.15532.829933.7542
152.83551.30973.34863.2308-1.97718.6151-0.5187-0.64260.1830.9227-0.4671-0.14291.2702-0.53080.65980.52970.1086-0.05160.47620.05260.51119.08144.594933.9448
162.91182.42421.59643.45362.98329.350.0574-0.35330.2565-0.3824-0.40521.15810.8509-1.17480.3890.277-0.0562-0.00760.2958-0.02080.3779-4.741215.0764-2.7832
179.1363-2.8151-1.49037.3234-0.74362.1098-0.32150.66580.3298-0.4201-0.51250.07260.0317-0.20420.87580.2462-0.0018-0.06350.3137-0.04690.316421.023524.246333.208
189.22833.25570.71532.0542.78247.1122-0.1676-0.14941.1149-0.96360.51140.0369-1.0846-1.1022-0.00370.63380.0552-0.17590.36480.01040.329813.100120.061330.4313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 89 )
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 30 )
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 44 )
11X-RAY DIFFRACTION11chain 'B' and (resid 45 through 57 )
12X-RAY DIFFRACTION12chain 'B' and (resid 58 through 77 )
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 89 )
14X-RAY DIFFRACTION14chain 'B' and (resid 90 through 97 )
15X-RAY DIFFRACTION15chain 'B' and (resid 98 through 104 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 14 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 6 )
18X-RAY DIFFRACTION18chain 'D' and (resid 7 through 13 )

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